From e2d3646c53acabc77e5e7d30e7f8aceeecfc3401 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:26:53 -0400 Subject: [PATCH 1/7] Add drug-to-disease template for testing --- src/ontogpt/templates/drug_to_disease.py | 258 +++++++++++++++++++++ src/ontogpt/templates/drug_to_disease.yaml | 66 ++++++ 2 files changed, 324 insertions(+) create mode 100644 src/ontogpt/templates/drug_to_disease.py create mode 100644 src/ontogpt/templates/drug_to_disease.yaml diff --git a/src/ontogpt/templates/drug_to_disease.py b/src/ontogpt/templates/drug_to_disease.py new file mode 100644 index 000000000..939afd1e3 --- /dev/null +++ b/src/ontogpt/templates/drug_to_disease.py @@ -0,0 +1,258 @@ +from __future__ import annotations +from datetime import ( + datetime, + date +) +from decimal import Decimal +from enum import Enum +import re +import sys +from typing import ( + Any, + ClassVar, + List, + Literal, + Dict, + Optional, + Union +) +from pydantic.version import VERSION as PYDANTIC_VERSION +if int(PYDANTIC_VERSION[0])>=2: + from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + field_validator + ) +else: + from pydantic import ( + BaseModel, + Field, + validator + ) + +metamodel_version = "None" +version = "None" + + +class ConfiguredBaseModel(BaseModel): + model_config = ConfigDict( + validate_assignment = True, + validate_default = True, + extra = "forbid", + arbitrary_types_allowed = True, + use_enum_values = True, + strict = False, + ) + pass + + + + +class LinkMLMeta(RootModel): + root: Dict[str, Any] = {} + model_config = ConfigDict(frozen=True) + + def __getattr__(self, key:str): + return getattr(self.root, key) + + def __getitem__(self, key:str): + return self.root[key] + + def __setitem__(self, key:str, value): + self.root[key] = value + + def __contains__(self, key:str) -> bool: + return key in self.root + + +linkml_meta = LinkMLMeta({'default_prefix': 'drug_to_disease', + 'default_range': 'string', + 'description': 'A template for extracting relationships between drugs and ' + 'diseases', + 'id': 'http://w3id.org/ontogpt/drug', + 'imports': ['linkml:types', 'core'], + 'license': 'https://creativecommons.org/publicdomain/zero/1.0/', + 'name': 'drug_to_disease', + 'prefixes': {'HGNC': {'prefix_prefix': 'HGNC', + 'prefix_reference': 'http://identifiers.org/hgnc/'}, + 'MESH': {'prefix_prefix': 'MESH', + 'prefix_reference': 'http://identifiers.org/mesh/'}, + 'drug': {'prefix_prefix': 'drug', + 'prefix_reference': 'http://w3id.org/ontogpt/drug/'}, + 'linkml': {'prefix_prefix': 'linkml', + 'prefix_reference': 'https://w3id.org/linkml/'}, + 'rdf': {'prefix_prefix': 'rdf', + 'prefix_reference': 'http://www.w3.org/1999/02/22-rdf-syntax-ns#'}}, + 'source_file': 'src/ontogpt/templates/drug_to_disease.yaml', + 'title': 'Drug to Disease Extraction Template'} ) + +class NullDataOptions(str, Enum): + UNSPECIFIED_METHOD_OF_ADMINISTRATION = "UNSPECIFIED_METHOD_OF_ADMINISTRATION" + NOT_APPLICABLE = "NOT_APPLICABLE" + NOT_MENTIONED = "NOT_MENTIONED" + + + +class ExtractionResult(ConfiguredBaseModel): + """ + A result of extracting knowledge on text + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) + + input_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_id', 'domain_of': ['ExtractionResult']} }) + input_title: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_title', 'domain_of': ['ExtractionResult']} }) + input_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'input_text', 'domain_of': ['ExtractionResult']} }) + raw_completion_output: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'raw_completion_output', 'domain_of': ['ExtractionResult']} }) + prompt: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'prompt', 'domain_of': ['ExtractionResult']} }) + extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'extracted_object', 'domain_of': ['ExtractionResult']} }) + named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'named_entities', 'domain_of': ['ExtractionResult']} }) + + +class NamedEntity(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) + + id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'comments': ['this is populated during the grounding and normalization step'], + 'domain_of': ['NamedEntity', 'Publication']} }) + label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', + 'aliases': ['name'], + 'domain_of': ['NamedEntity'], + 'slot_uri': 'rdfs:label'} }) + + +class CompoundExpression(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) + + pass + + +class Triple(CompoundExpression): + """ + Abstract parent for Relation Extraction tasks + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) + + subject: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject', 'domain_of': ['Triple', 'DrugToDisease']} }) + predicate: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['Triple', 'DrugToDisease']} }) + object: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object', 'domain_of': ['Triple', 'DrugToDisease']} }) + qualifier: Optional[str] = Field(None, description="""A qualifier for the statements, e.g. \"NOT\" for negation""", json_schema_extra = { "linkml_meta": {'alias': 'qualifier', 'domain_of': ['Triple']} }) + subject_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the subject of the statement, e.g. \"high dose\" or \"intravenously administered\"""", json_schema_extra = { "linkml_meta": {'alias': 'subject_qualifier', 'domain_of': ['Triple']} }) + object_qualifier: Optional[str] = Field(None, description="""An optional qualifier or modifier for the object of the statement, e.g. \"severe\" or \"with additional complications\"""", json_schema_extra = { "linkml_meta": {'alias': 'object_qualifier', 'domain_of': ['Triple']} }) + + +class TextWithTriples(ConfiguredBaseModel): + """ + A text containing one or more relations of the Triple type. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) + + publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) + triples: Optional[List[Triple]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'triples', 'domain_of': ['TextWithTriples']} }) + + +class TextWithEntity(ConfiguredBaseModel): + """ + A text containing one or more instances of a single type of entity. + """ + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) + + publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) + entities: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'entities', 'domain_of': ['TextWithEntity']} }) + + +class RelationshipType(NamedEntity): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core', + 'id_prefixes': ['RO', 'biolink']}) + + id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'comments': ['this is populated during the grounding and normalization step'], + 'domain_of': ['NamedEntity', 'Publication']} }) + label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', + 'aliases': ['name'], + 'domain_of': ['NamedEntity'], + 'slot_uri': 'rdfs:label'} }) + + +class Publication(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) + + id: Optional[str] = Field(None, description="""The publication identifier""", json_schema_extra = { "linkml_meta": {'alias': 'id', 'domain_of': ['NamedEntity', 'Publication']} }) + title: Optional[str] = Field(None, description="""The title of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'title', 'domain_of': ['Publication']} }) + abstract: Optional[str] = Field(None, description="""The abstract of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'abstract', 'domain_of': ['Publication']} }) + combined_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'combined_text', 'domain_of': ['Publication']} }) + full_text: Optional[str] = Field(None, description="""The full text of the publication""", json_schema_extra = { "linkml_meta": {'alias': 'full_text', 'domain_of': ['Publication']} }) + + +class AnnotatorResult(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) + + subject_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject_text', 'domain_of': ['AnnotatorResult']} }) + object_id: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_id', 'domain_of': ['AnnotatorResult']} }) + object_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_text', 'domain_of': ['AnnotatorResult']} }) + + +class DrugMechanism(ConfiguredBaseModel): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/drug', 'tree_root': True}) + + diseases: Optional[str] = Field(None, description="""A semicolon-separated list of diseases mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'diseases', 'domain_of': ['DrugMechanism']} }) + drug: Optional[str] = Field(None, description="""A semicolon-separated list of drugs mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'drug', 'domain_of': ['DrugMechanism']} }) + drug_to_disease_relationships: Optional[List[DrugToDisease]] = Field(default_factory=list, description="""A semicolon-separated list of relationships, where each is a triple connecting a drug to a disease. Each relationship should have a type (predicate) and two entities (subject and object). The predicate may be one of the following: 'treats', 'causes', 'prevents'. For example: \"Drug1 treats Disease1; Drug2 causes Disease2\".""", json_schema_extra = { "linkml_meta": {'alias': 'drug_to_disease_relationships', 'domain_of': ['DrugMechanism']} }) + + +class Disease(NamedEntity): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators', + 'value': 'sqlite:obo:mondo'}}, + 'from_schema': 'http://w3id.org/ontogpt/drug', + 'id_prefixes': ['MONDO']}) + + id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'comments': ['this is populated during the grounding and normalization step'], + 'domain_of': ['NamedEntity', 'Publication']} }) + label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', + 'aliases': ['name'], + 'domain_of': ['NamedEntity'], + 'slot_uri': 'rdfs:label'} }) + + +class Drug(NamedEntity): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'annotations': {'annotators': {'tag': 'annotators', + 'value': 'sqlite:obo:drugbank, ' + 'sqlite:obo:chebi'}}, + 'from_schema': 'http://w3id.org/ontogpt/drug', + 'id_prefixes': ['DRUGBANK', 'CHEBI']}) + + id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'comments': ['this is populated during the grounding and normalization step'], + 'domain_of': ['NamedEntity', 'Publication']} }) + label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', + 'aliases': ['name'], + 'domain_of': ['NamedEntity'], + 'slot_uri': 'rdfs:label'} }) + + +class DrugToDisease(CompoundExpression): + linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/drug'}) + + subject: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'subject', 'domain_of': ['Triple', 'DrugToDisease']} }) + predicate: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'predicate', 'domain_of': ['Triple', 'DrugToDisease']} }) + object: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object', 'domain_of': ['Triple', 'DrugToDisease']} }) + + +# Model rebuild +# see https://pydantic-docs.helpmanual.io/usage/models/#rebuilding-a-model +ExtractionResult.model_rebuild() +NamedEntity.model_rebuild() +CompoundExpression.model_rebuild() +Triple.model_rebuild() +TextWithTriples.model_rebuild() +TextWithEntity.model_rebuild() +RelationshipType.model_rebuild() +Publication.model_rebuild() +AnnotatorResult.model_rebuild() +DrugMechanism.model_rebuild() +Disease.model_rebuild() +Drug.model_rebuild() +DrugToDisease.model_rebuild() + diff --git a/src/ontogpt/templates/drug_to_disease.yaml b/src/ontogpt/templates/drug_to_disease.yaml new file mode 100644 index 000000000..823e16ac0 --- /dev/null +++ b/src/ontogpt/templates/drug_to_disease.yaml @@ -0,0 +1,66 @@ +id: http://w3id.org/ontogpt/drug +name: drug_to_disease +title: Drug to Disease Extraction Template +description: >- + A template for extracting relationships between drugs and diseases +license: https://creativecommons.org/publicdomain/zero/1.0/ +prefixes: + rdf: http://www.w3.org/1999/02/22-rdf-syntax-ns# + HGNC: http://identifiers.org/hgnc/ + MESH: http://identifiers.org/mesh/ + drug: http://w3id.org/ontogpt/drug/ + linkml: https://w3id.org/linkml/ + +default_prefix: drug_to_disease +default_range: string + +imports: + - linkml:types + - core + +classes: + DrugMechanism: + tree_root: true + attributes: + diseases: + description: >- + A semicolon-separated list of diseases mentioned in the text. + range: Disease + drug: + description: >- + A semicolon-separated list of drugs mentioned in the text. + range: Drug + drug_to_disease_relationships: + description: >- + A semicolon-separated list of relationships, where each is a triple + connecting a drug to a disease. Each relationship should have a + type (predicate) and two entities (subject and object). The predicate + may be one of the following: 'treats', 'causes', 'prevents'. + For example: "Drug1 treats Disease1; Drug2 causes Disease2". + multivalued: true + range: DrugToDisease + + Disease: + is_a: NamedEntity + id_prefixes: + - MONDO + annotations: + annotators: sqlite:obo:mondo + + Drug: + is_a: NamedEntity + id_prefixes: + - DRUGBANK + - CHEBI + annotations: + annotators: sqlite:obo:drugbank, sqlite:obo:chebi + + DrugToDisease: + is_a: CompoundExpression + attributes: + subject: + range: Drug + predicate: + range: string + object: + range: Disease From 71fcdb5ba4640b6976c807ebcfd1e120e6fd4ff8 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:28:00 -0400 Subject: [PATCH 2/7] Update poetry lock --- poetry.lock | 1379 +++++++++++++++++++++++++++------------------------ 1 file changed, 735 insertions(+), 644 deletions(-) diff --git a/poetry.lock b/poetry.lock index 89655c505..225edc949 100644 --- a/poetry.lock +++ b/poetry.lock @@ -33,98 +33,98 @@ files = [ 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"zipp-3.19.2-py3-none-any.whl", hash = "sha256:f091755f667055f2d02b32c53771a7a6c8b47e1fdbc4b72a8b9072b3eef8015c"}, - {file = "zipp-3.19.2.tar.gz", hash = "sha256:bf1dcf6450f873a13e952a29504887c89e6de7506209e5b1bcc3460135d4de19"}, + {file = "zipp-3.20.0-py3-none-any.whl", hash = "sha256:58da6168be89f0be59beb194da1250516fdaa062ccebd30127ac65d30045e10d"}, + {file = "zipp-3.20.0.tar.gz", hash = "sha256:0145e43d89664cfe1a2e533adc75adafed82fe2da404b4bbb6b026c0157bdb31"}, ] [package.extras] From 6c1a58b91c38cc096c66c046f3dd41d33890922a Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:29:19 -0400 Subject: [PATCH 3/7] Update Makefile re: gen-pydantic --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 7f41d7b62..8a1a1afcb 100644 --- a/Makefile +++ b/Makefile @@ -27,10 +27,10 @@ get_version: $(RUN) python -c "import ontogpt;print('.'.join((ontogpt.__version__).split('.', 3)[:3]))" $(TEMPLATE_DIR)/%.py: src/$(PACKAGE)/templates/%.yaml - $(RUN) gen-pydantic --pydantic-version 2 $< > $@.tmp && mv $@.tmp $@ + $(RUN) gen-pydantic $< > $@.tmp && mv $@.tmp $@ %.py: %.yaml - $(RUN) gen-pydantic --pydantic-version 2 $< > $@ + $(RUN) gen-pydantic $< > $@ #all_images: $(patsubst %, docs/images/%.png, $(ENTRY_CLASSES)) #docs/images/%.png: From 75113a4ff5522b030e7d66d4c860681914a25b30 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:29:37 -0400 Subject: [PATCH 4/7] Update drug_to_disease template --- src/ontogpt/templates/drug_to_disease.py | 59 ++++++++++++---------- src/ontogpt/templates/drug_to_disease.yaml | 2 +- 2 files changed, 34 insertions(+), 27 deletions(-) diff --git a/src/ontogpt/templates/drug_to_disease.py b/src/ontogpt/templates/drug_to_disease.py index 939afd1e3..e7dab2935 100644 --- a/src/ontogpt/templates/drug_to_disease.py +++ b/src/ontogpt/templates/drug_to_disease.py @@ -16,22 +16,13 @@ Optional, Union ) -from pydantic.version import VERSION as PYDANTIC_VERSION -if int(PYDANTIC_VERSION[0])>=2: - from pydantic import ( - BaseModel, - ConfigDict, - Field, - RootModel, - field_validator - ) -else: - from pydantic import ( - BaseModel, - Field, - validator - ) - +from pydantic import ( + BaseModel, + ConfigDict, + Field, + RootModel, + field_validator +) metamodel_version = "None" version = "None" @@ -107,17 +98,20 @@ class ExtractionResult(ConfiguredBaseModel): raw_completion_output: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'raw_completion_output', 'domain_of': ['ExtractionResult']} }) prompt: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'prompt', 'domain_of': ['ExtractionResult']} }) extracted_object: Optional[Any] = Field(None, description="""The complex objects extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'extracted_object', 'domain_of': ['ExtractionResult']} }) - named_entities: Optional[List[Any]] = Field(default_factory=list, description="""Named entities extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'named_entities', 'domain_of': ['ExtractionResult']} }) + named_entities: Optional[List[Any]] = Field(None, description="""Named entities extracted from the text""", json_schema_extra = { "linkml_meta": {'alias': 'named_entities', 'domain_of': ['ExtractionResult']} }) class NamedEntity(ConfiguredBaseModel): linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'abstract': True, 'from_schema': 'http://w3id.org/ontogpt/core'}) id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, 'comments': ['this is populated during the grounding and normalization step'], 'domain_of': ['NamedEntity', 'Publication']} }) label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', 'aliases': ['name'], + 'annotations': {'owl': {'tag': 'owl', + 'value': 'AnnotationProperty, AnnotationAssertion'}}, 'domain_of': ['NamedEntity'], 'slot_uri': 'rdfs:label'} }) @@ -148,8 +142,10 @@ class TextWithTriples(ConfiguredBaseModel): """ linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) - publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) - triples: Optional[List[Triple]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'triples', 'domain_of': ['TextWithTriples']} }) + publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', + 'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, + 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) + triples: Optional[List[Triple]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'triples', 'domain_of': ['TextWithTriples']} }) class TextWithEntity(ConfiguredBaseModel): @@ -158,8 +154,10 @@ class TextWithEntity(ConfiguredBaseModel): """ linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/core'}) - publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) - entities: Optional[List[str]] = Field(default_factory=list, json_schema_extra = { "linkml_meta": {'alias': 'entities', 'domain_of': ['TextWithEntity']} }) + publication: Optional[Publication] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'publication', + 'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, + 'domain_of': ['TextWithTriples', 'TextWithEntity']} }) + entities: Optional[List[str]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'entities', 'domain_of': ['TextWithEntity']} }) class RelationshipType(NamedEntity): @@ -167,10 +165,13 @@ class RelationshipType(NamedEntity): 'id_prefixes': ['RO', 'biolink']}) id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, 'comments': ['this is populated during the grounding and normalization step'], 'domain_of': ['NamedEntity', 'Publication']} }) label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', 'aliases': ['name'], + 'annotations': {'owl': {'tag': 'owl', + 'value': 'AnnotationProperty, AnnotationAssertion'}}, 'domain_of': ['NamedEntity'], 'slot_uri': 'rdfs:label'} }) @@ -193,12 +194,12 @@ class AnnotatorResult(ConfiguredBaseModel): object_text: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'object_text', 'domain_of': ['AnnotatorResult']} }) -class DrugMechanism(ConfiguredBaseModel): +class Article(ConfiguredBaseModel): linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/drug', 'tree_root': True}) - diseases: Optional[str] = Field(None, description="""A semicolon-separated list of diseases mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'diseases', 'domain_of': ['DrugMechanism']} }) - drug: Optional[str] = Field(None, description="""A semicolon-separated list of drugs mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'drug', 'domain_of': ['DrugMechanism']} }) - drug_to_disease_relationships: Optional[List[DrugToDisease]] = Field(default_factory=list, description="""A semicolon-separated list of relationships, where each is a triple connecting a drug to a disease. Each relationship should have a type (predicate) and two entities (subject and object). The predicate may be one of the following: 'treats', 'causes', 'prevents'. For example: \"Drug1 treats Disease1; Drug2 causes Disease2\".""", json_schema_extra = { "linkml_meta": {'alias': 'drug_to_disease_relationships', 'domain_of': ['DrugMechanism']} }) + diseases: Optional[str] = Field(None, description="""A semicolon-separated list of diseases mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'diseases', 'domain_of': ['Article']} }) + drug: Optional[str] = Field(None, description="""A semicolon-separated list of drugs mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'drug', 'domain_of': ['Article']} }) + drug_to_disease_relationships: Optional[List[DrugToDisease]] = Field(None, description="""A semicolon-separated list of relationships, where each is a triple connecting a drug to a disease. Each relationship should have a type (predicate) and two entities (subject and object). The predicate may be one of the following: 'treats', 'causes', 'prevents'. For example: \"Drug1 treats Disease1; Drug2 causes Disease2\".""", json_schema_extra = { "linkml_meta": {'alias': 'drug_to_disease_relationships', 'domain_of': ['Article']} }) class Disease(NamedEntity): @@ -208,10 +209,13 @@ class Disease(NamedEntity): 'id_prefixes': ['MONDO']}) id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, 'comments': ['this is populated during the grounding and normalization step'], 'domain_of': ['NamedEntity', 'Publication']} }) label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', 'aliases': ['name'], + 'annotations': {'owl': {'tag': 'owl', + 'value': 'AnnotationProperty, AnnotationAssertion'}}, 'domain_of': ['NamedEntity'], 'slot_uri': 'rdfs:label'} }) @@ -224,10 +228,13 @@ class Drug(NamedEntity): 'id_prefixes': ['DRUGBANK', 'CHEBI']}) id: str = Field(..., description="""A unique identifier for the named entity""", json_schema_extra = { "linkml_meta": {'alias': 'id', + 'annotations': {'prompt.skip': {'tag': 'prompt.skip', 'value': 'true'}}, 'comments': ['this is populated during the grounding and normalization step'], 'domain_of': ['NamedEntity', 'Publication']} }) label: Optional[str] = Field(None, description="""The label (name) of the named thing""", json_schema_extra = { "linkml_meta": {'alias': 'label', 'aliases': ['name'], + 'annotations': {'owl': {'tag': 'owl', + 'value': 'AnnotationProperty, AnnotationAssertion'}}, 'domain_of': ['NamedEntity'], 'slot_uri': 'rdfs:label'} }) @@ -251,7 +258,7 @@ class DrugToDisease(CompoundExpression): RelationshipType.model_rebuild() Publication.model_rebuild() AnnotatorResult.model_rebuild() -DrugMechanism.model_rebuild() +Article.model_rebuild() Disease.model_rebuild() Drug.model_rebuild() DrugToDisease.model_rebuild() diff --git a/src/ontogpt/templates/drug_to_disease.yaml b/src/ontogpt/templates/drug_to_disease.yaml index 823e16ac0..ceb76608e 100644 --- a/src/ontogpt/templates/drug_to_disease.yaml +++ b/src/ontogpt/templates/drug_to_disease.yaml @@ -19,7 +19,7 @@ imports: - core classes: - DrugMechanism: + Article: tree_root: true attributes: diseases: From 49970ed548dfb7e7e6bc0fbf4cf30082c89c2ac4 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:31:07 -0400 Subject: [PATCH 5/7] Update drug_to_disease template again --- src/ontogpt/templates/drug_to_disease.py | 4 ++-- src/ontogpt/templates/drug_to_disease.yaml | 2 ++ 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/ontogpt/templates/drug_to_disease.py b/src/ontogpt/templates/drug_to_disease.py index e7dab2935..242d9ea93 100644 --- a/src/ontogpt/templates/drug_to_disease.py +++ b/src/ontogpt/templates/drug_to_disease.py @@ -197,8 +197,8 @@ class AnnotatorResult(ConfiguredBaseModel): class Article(ConfiguredBaseModel): linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'from_schema': 'http://w3id.org/ontogpt/drug', 'tree_root': True}) - diseases: Optional[str] = Field(None, description="""A semicolon-separated list of diseases mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'diseases', 'domain_of': ['Article']} }) - drug: Optional[str] = Field(None, description="""A semicolon-separated list of drugs mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'drug', 'domain_of': ['Article']} }) + diseases: Optional[List[str]] = Field(None, description="""A semicolon-separated list of diseases mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'diseases', 'domain_of': ['Article']} }) + drug: Optional[List[str]] = Field(None, description="""A semicolon-separated list of drugs mentioned in the text.""", json_schema_extra = { "linkml_meta": {'alias': 'drug', 'domain_of': ['Article']} }) drug_to_disease_relationships: Optional[List[DrugToDisease]] = Field(None, description="""A semicolon-separated list of relationships, where each is a triple connecting a drug to a disease. Each relationship should have a type (predicate) and two entities (subject and object). The predicate may be one of the following: 'treats', 'causes', 'prevents'. For example: \"Drug1 treats Disease1; Drug2 causes Disease2\".""", json_schema_extra = { "linkml_meta": {'alias': 'drug_to_disease_relationships', 'domain_of': ['Article']} }) diff --git a/src/ontogpt/templates/drug_to_disease.yaml b/src/ontogpt/templates/drug_to_disease.yaml index ceb76608e..8c2e98036 100644 --- a/src/ontogpt/templates/drug_to_disease.yaml +++ b/src/ontogpt/templates/drug_to_disease.yaml @@ -25,10 +25,12 @@ classes: diseases: description: >- A semicolon-separated list of diseases mentioned in the text. + multivalued: true range: Disease drug: description: >- A semicolon-separated list of drugs mentioned in the text. + multivalued: true range: Drug drug_to_disease_relationships: description: >- From 7391b8a408da02f502b4e20591efa27a74f452fc Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:49:27 -0400 Subject: [PATCH 6/7] Add ephemeral cache to mapping --- src/ontogpt/engines/knowledge_engine.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/src/ontogpt/engines/knowledge_engine.py b/src/ontogpt/engines/knowledge_engine.py index 3dc6e64c6..c8d482db7 100644 --- a/src/ontogpt/engines/knowledge_engine.py +++ b/src/ontogpt/engines/knowledge_engine.py @@ -106,6 +106,9 @@ class KnowledgeEngine(ABC): mappers: Optional[List[BasicOntologyInterface]] = None """List of concept mappers, to assist in grounding to desired ID prefix""" + map_cache: Dict[str, str] = field(default_factory=dict) + """Cache of mappings obtained using the specified mappers.""" + labelers: Optional[List[BasicOntologyInterface]] = None """Labelers that map CURIEs to labels""" @@ -395,6 +398,12 @@ def map_identifier(self, input_id: str, cls: ClassDefinition) -> Iterator[str]: :param cls: :return: """ + if input_id not in self.map_cache: + self.map_cache[input_id] = [] + else: + for obj_id in self.map_cache[input_id]: + yield obj_id + try: if input_id.startswith("http://purl.bioontology.org/ontology"): # TODO: this should be fixed upstream in OAK @@ -416,6 +425,7 @@ def map_identifier(self, input_id: str, cls: ClassDefinition) -> Iterator[str]: for mapper in self.mappers: if isinstance(mapper, MappingProviderInterface): for mapping in mapper.sssom_mappings([input_id]): + self.map_cache[input_id].append(str(mapping.object_id)) yield str(mapping.object_id) else: raise ValueError(f"Unknown mapper type {mapper}") From 6a516737b55ce1e279b857751319450716b64d5d Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Sun, 11 Aug 2024 13:58:24 -0400 Subject: [PATCH 7/7] Fix typing issues --- src/ontogpt/engines/knowledge_engine.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/ontogpt/engines/knowledge_engine.py b/src/ontogpt/engines/knowledge_engine.py index c8d482db7..ae40c7537 100644 --- a/src/ontogpt/engines/knowledge_engine.py +++ b/src/ontogpt/engines/knowledge_engine.py @@ -106,7 +106,7 @@ class KnowledgeEngine(ABC): mappers: Optional[List[BasicOntologyInterface]] = None """List of concept mappers, to assist in grounding to desired ID prefix""" - map_cache: Dict[str, str] = field(default_factory=dict) + map_cache: Dict[str, List[str]] = field(default_factory=dict) """Cache of mappings obtained using the specified mappers.""" labelers: Optional[List[BasicOntologyInterface]] = None @@ -425,7 +425,7 @@ def map_identifier(self, input_id: str, cls: ClassDefinition) -> Iterator[str]: for mapper in self.mappers: if isinstance(mapper, MappingProviderInterface): for mapping in mapper.sssom_mappings([input_id]): - self.map_cache[input_id].append(str(mapping.object_id)) + (self.map_cache[input_id]).append(str(mapping.object_id)) yield str(mapping.object_id) else: raise ValueError(f"Unknown mapper type {mapper}")